title: CP-EX-370-BalbC-p53null-2153F_GAGCTGAA_S20_L004

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Resulting fastq files were aligned to the mouse mm10 reference genome using the STAR aligner algorithm
BAM files were sorted and indexed using Samtools and quality control was performed using Picard
Transcript read counts were determined was performed using Salmon
Genome_build: mm10
Supplementary_files_format_and_content: Salmon quantified, upper-quartile normalized read-counts.

growth_protocol: Tumors were orthotopically injected in sygeneic hosts. Tumors were allowed to progress to a 5mm diameter and opon which mice were randomized to study arms.

extract_protocol:
RNA was extracted using Qiagen Rneasy kits. mRNA quality was assessed using the Agilent Bioanalyzer.
Libraries for mRNA-seq made using total RNA and the Illumina TruSeq mRNA sample preparation kit
Paired end (2x50bp) sequencing was performed on the Illumina HiSeq 2000/2500 sequencer at the UNC High Throughput Sequencing Facility

treatment_protocol: Antibody was delivered using 100ul volumes and injected intraperitoneally bi-weekly for the following: anti-CTLA4 (125 ug, bioxcel BE0164), anti-PD1 (10mg/kg, bioxcel BE0146).

value: Tumor

value: BalbC


title: CP-EX-363-T11_UV

status: Public on Nov 13 2019

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

value: CellLine

tag: strain


title: CP-2355

library_source: transcriptomic

molecule: total RNA

tag: model

tag: class

value: resistant

tag: time

value: end

tag: therapy

value: tumor


title: CP-EX-375-BalbCp53null2336R_ACCACTGT_S10_L003


title: CP-EX-362-KPB25Luv

value: FVB


title: CP-EX-369-BalbC-p53null-9263-3F_AGCAGGAA_S19_L004


title: WP_AdCre_aHA_repl2

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Mouse Reference Genome (mm9) or Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (v1.5) and MACS (v1.4) peak caller. Only peaks called by both algorithms were used for further analysis.
Genome_build: mm9 (MMECs), hg19 (MCF7)
Supplementary_files_format_and_content: filtered.intersect files contain peaks called by both peak calling algorithms in bed format

source_name: Primary mouse mammary epithelial cells

extract_protocol:
Chromatin immunoprecipitations were performed as described previously, with adaptations (Schmidt et al., 2009). In short, cells were crosslinked in solution A (pH 7.4, 50mM Hepes, 100mM NaCl, 1mM EDTA, 0.5M EGTA) containing 2mM DSG for 35 minutes, then formaldehyde was added to a final concentration of 1% and incubated for another 10 minutes. After addition of Glycine to a final concentration of 125mM to quench the crosslinking reaction and washing with PBS, cells were collected. The Bioruptor Pico (Diagenode) was used for sonication. For ChIP, antibodies were used to detect the HA-tag (25ug, 05-904, Millipore) and ERa (10ug, sc-543, Santa Cruz) with 100 ml Protein A magnetic beads (Thermo Scientific).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

tag: cell type

value: Primary MMECs

tag: genotype

tag: chip antibody

value: aHA (Millipore, catalog# 05-904)

tag: treatment

value: AdCre transduction, harvested after 72hrs


title: CP-2372

value: no


title: T11-Apobec


title: T-11-CellLine-Parental


title: CP-EX-361-KPB25L_Apobec


title: CP-EX-381-FVB-NORMAL-MAMM-VAL_GACAGTGC_S2_L001

value: Normal Mammary


title: WP_HA-hERa_AdCre_aHA_repl2


title: CP-EX-380-BalbC-NORMAL-MAMM-VAL_CGGATTGC_S7_L002


title: WP_AdCre_aHA_repl1


title: CP-2162

value: sensitive


title: WP_HA-hERa_AdCre_aHA_repl1


title: CP-EX-374-BalbCp53null2225L_GCCACATA_S11_L003


title: KPB-25L-Parental


title: CP-2364


title: CP-EX-373-BalbCp53null2224L_ATCATTCC_S9_L003


title: WP_HA-mERa_AdCre_aHA_repl2


title: WP_HA-mERa_AdCre_aHA_repl1


title: CP-2374

value: 3 day


title: CP-2373


title: CP-2375


title: CP-2376


title: CP-2371


title: WP_HA-mERa_AdCre_MMECs_E2_repl1

data_processing:
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)
Sequencing data was aligned to GRCh38 (MCF7) or GRCm38 (MMECs) using TopHat and number of reads per gene were measured with HTSeq count.
Read counts were corrected for differences in sequencing depth by using DESeqs median-of-ratios and the normalized counts were log2-transformed.
Genome_build: GRCh38 (MCF7), GRCm38 (MMECs)
Supplementary_files_format_and_content: Expression table of samples (columns) by transcript (rows) reporting normalized counts.

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.).

value: AdCre transduction followed by 72hrs hormone deprivation; 6hrs Estradiol


title: CP-2261


title: CP-2260


title: CP-2370


title: CP-2265


title: CP-2264


title: CP-2292


title: CP-2363


title: CP-2412

value: 7 day


title: CP-2263


title: CP-2293


title: CP-2278


title: CP-2361


title: CP-2409


title: CP-2411


title: CP-2290


title: CP-2362


title: CP-2279


title: CP-2281


title: CP-2420


title: CP-2417


title: CP-2404


title: CP-2418


title: CP-2356


title: CP-2402


title: CP-2280


title: CP-2410


title: CP-2259


title: CP-2258


title: CP-2369


title: CP-2419


title: CP-2379


title: CP-2262


title: CP-2407


title: CP-2377


title: CP-2408


title: CP-2380


title: CP-2405


title: CP-2403


title: CP-2401


title: CP-2299


title: CP-2300


title: CP-1915

value: unknown


title: CP-1917


title: CP-2301


title: CP-1916


title: CP-2406


title: CP-1913


title: CP-1912


title: CP-1911


title: CP-1910


title: CP-2298


title: CP-1914


title: CP-1909


title: CP-1908


title: CP-1899

value: PyMT


title: CP-1900


title: CP-1898


title: CP-1897


title: CP-2378


title: CP-1896


title: CP-2344


title: CP-2342


title: CP-2311


title: CP-2343


title: CP-2345


title: CP-2335


title: CP-2336


title: CP-2313


title: CP-2319


title: CP-2326


title: CP-2312


title: CP-2337


title: CP-2329


title: CP-2320


title: CP-2348


title: CP-2328

value: nt


title: CP-2381

value: in vitro


title: CP-2166


title: CP-2321


title: CP-2159


title: CP-2327


title: CP-2350

value: resistant


title: CP-2351


title: CP-2318


title: CP-2352


title: CP-2349


title: CP-1681

value: end


title: CP-1975

value: tumor


title: CP-2053


title: CP-2054


title: CP-2046


title: CP-2045


title: CP-1680


title: CP-2310


title: CP-2170


title: CP-2334


title: CP-2048


title: CP-2047


title: CP-2118


title: CP-2050


title: CP-2127


title: CP-2049


title: CP-2123


title: CP-2128


title: CP-2113


title: CP-2115


title: CP-2061


title: CP-2109


title: CP-2120


title: CP-2129


title: CP-2062


title: CP-2066


title: CP-2169


title: CP-2063


title: CP-2065


title: CP-1673


title: CP-2064


title: CP-2145


title: CP-2144


title: CP-2055


title: CP-2057


title: CP-2056


title: CP-2052


title: CP-2051


title: CP-2143


title: CP-2142


title: CP-2273


title: CP-2271


title: CP-2272


title: CP-2270


title: CP-2257


title: CP-2256


title: CP-2168


title: CP-2255


title: CP-1675


title: CP-2254


title: CP-1949

value: NML-FVB


title: CP-1676


title: CP-1678

value: NML-BALBC


title: CP-1331


title: CP-1948


title: CP-1946


title: CP-1657

value: KPB-Primary


title: CP-1656


title: CP-1679


title: CP-1947


title: CP-1259


title: CP-1252


title: CP-1271


title: CP-1660


title: CP-1253


title: CP-1255


title: CP-1659


title: CP-1258


title: CP-1267


title: CP-1677


title: CP-1265


title: CP-1264


title: CP-1256


title: CP-1261


title: CP-1266


title: CP-1250


title: CP-1262


title: CP-1251


title: CP-2165


title: CP-1257


title: CP-2267


title: CP-2269


title: CP-1270


title: CP-2268


title: CP-2266


title: CP-1268


title: CP-1269


title: CP-2163


title: CP-1260


title: CP-2276


title: CP-2297


title: CP-2275


title: CP-2296


title: CP-2285


title: CP-2282


title: CP-2283


title: CP-2284


title: CP-2295


title: CP-2277


title: CP-2274


title: CP-2339


title: CP-2341


title: CP-2315


title: CP-2382


title: CP-2325


title: CP-2317


title: CP-2009


title: CP-2010


title: CP-2366


title: CP-2314


title: CP-2316


title: CP-2330


title: CP-2332


title: CP-2015


title: CP-2368


title: CP-2333


title: CP-2006


title: CP-2294


title: CP-2005


title: CP-2111

source_name: kpb25l|5mm (3 day post treat)|pd1/ctla4|170706_UNC18-D00493_0430_ACBBR1ANXX_TGACCA_S7_L008


title: CP-2141

source_name: kpb25l|5mm (3 day post treat)|pd1/ctla4|170728_UNC17-D00216_0461_ACBCGAANXX_TAGCTT_S21_L005


title: CP-2018


title: CP-2340


title: CP-2338


title: CP-2008


title: CP-2011

source_name: kpb25L|5mm (3 day post treat)|no|170505_UNC17-D00216_0440_ACAL2BANXX_ACTTGA_S4_L007


title: CP-2126

source_name: kpb25l|5mm (3 day post treat)|no|170706_UNC18-D00493_0430_ACBBR1ANXX_GTGGCC_S13_L004


title: CP-2121

source_name: kpb25l|5mm (3 day post treat)|pd1/ctla4|170706_UNC18-D00493_0430_ACBBR1ANXX_AGTTCC_S18_L005


title: CP-2020

source_name: kpb25l|5mm (3 day post treat)|pd1/ctla4|170505_UNC17-D00216_0440_ACAL2BANXX_GTCCGC_S15_L004


title: CP-2360


title: CP-2358


title: CP-2359


title: CP-2424


title: CP-2357


title: CP-2423


title: CP-2414


title: CP-2415


title: CP-2140

source_name: kpb25L|5mm (3 day post treat)|pd1/ctla4|170728_UNC17-D00216_0461_ACBCGAANXX_GATCAG_S22_L005


title: CP-2422


title: CP-1276


title: NCRNA111_RNA_2

type: RNA

city: Huddinge

first: Olga

last: Khorosjutina

department: Bioscience and nutrition

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Hybridized to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://www.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL files were normalized with quantile normalization plus scaling in Tiling Analysis Software  (TAS v1.1.02., Affymetrix), 2004 genome assembly, linear scale, target intensity: 100, band width:100.
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1.02  and contain linear values for each probe. F: forward strand, R: reverse strand.Text files contain linear signal  scores  for RNA levels. Expression_data.csv supplementary result  file is generated in Podbat, quantified further in Excel and  contains, in order: UniqueID, Systematic name, Chromosome, Left border, Right border, Strand, Description, WT1 (OK1(s)), WT2(OK2(s)), ncRNA111_1(OK3(s)), ncRNA111_2(OK4(s)), Signal to noise ratio (SNR) (aveWT-aveMUT)/(stdevWT+stdevMUT), absolute value  SNR, Fold change (aveMUT/aveWT), FOLD Change ( UP(+) DOWN (-))

label: biotin

organism: Schizosaccharomyces pombe

label_protocol: Biotin-labeled according to standard Affymetrix protocols.

growth_protocol: Cultures were grown at 30°C in YES media to mid-log phase.

extract_protocol: RNA was extracted using hot acid phenol and chloroform method. Cells were harvested by centrifugation at RT, resuspended in TES buffer (10mM Tris-Cl pH 7.5,  10mMEDTA,  0.5%SDS) and immediately combined with preheated to 65oC Phenol. After incubation (30min-1hour) at 65oC (vortex every 10 min), RNA was phenol-chloroform extracted and purified using RNeasy mini- kit( Qiagen). RNA quality was assessed using Agilent TAPE-station 2200(Agilent).

value: h90 SPNCRNA111.1::hphR


title: NCRNA111_RNA_1


title: CP-2413

value: no


title: CP-2421


title: WT_RNA_1

source_name: WT


title: CP-2416


title: WT_RNA_2


title: CP-2004

source_name: kpb25L|5mm (3 day post treat)|no|170505_UNC17-D00216_0440_ACAL2BANXX_ATCACG_S5_L008


title: CP-1275


title: CP-1274


title: CP-2171


title: CP-1273


title: CP-2308


title: CP-2306


title: CP-2160


title: CP-2158


title: C3TAG-159447


title: nonNeuron_AhrAgo_2

city: London

first: Vassilis

last: Pachnis

state: London

address: 1 Midland Road

department: Development and Homeostasis of the Nervous System Laboratory

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) in conjunction with the STAR alignment algorithm (version 2.5.2)  was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl GRCm38-release-89 transcriptome
Differential expression analysis was performed with the DESeq2 package (version 1.10.1) within the R programming environment (version 3.3.2)
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files containing TMM normalised data. Rows represent ensembl gene identifiers and columns represent individual samples.

extract_protocol:
Nuclear RNA was isolated using PureLink RNA Micro Kit (Invitrogen #12183016) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies, Inc.). Following quantification on a Qubit 3.0 fluorometer (Thermo Fisher Scientific, Inc.), cDNA was fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris, Inc.) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies, Inc.). A total of 7 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies, Inc.). The libraries were then normalized to 2.5 nM, pooled and loaded onto a HiSeq4000 (Illumina, Inc.) to generate 75bp single-end reads.

treatment_protocol: C57BL/6 mice were injected intraperitoneally with 3-methylcholanthrene (AhR agonist) or corn oil (control) 14 hours before nuclear isolation.

tag: environmental condition

value: specific pathogen-free (SPF)

value: AhR agonist (3-methylcholanthrene)

value: colon

value: non-neuronal

tag: molecule subtype

value: Nuclear mRNA


title: Neuron_Ctrl_4

value: Control (corn oil)

value: neuronal


title: nonNeuron_Ctrl_4


title: nonNeuron_Ctrl_2


title: nonNeuron_Ctrl_3


title: nonNeuron_AhrAgo_3


title: nonNeuron_Ctrl_1


title: nonNeuron_AhrAgo_4


title: Neuron_Ctrl_1


title: nonNeuron_AhrAgo_1


title: Neuron_AhrAgo_2


title: Neuron_AhrAgo_3


title: Neuron_AhrAgo_1


title: Neuron_Ctrl_2


title: Neuron_Ctrl_3


title: Human dermal fibroblasts_rep1

city: Chiba

first: Ryoko

last: Araki

address: Anagawa4-9-1, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences, National Institutes for Quantum and Radiological Science and Technology

hyb_protocol: Slides were hybridized to SurePrint G3 Human Gene Expression 8x60K v3 Microarray (Agilent) according to manufacturer’s protocols.

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263.

data_processing: Microarray results were extracted using Agilent Feature Extraction software v11.0 (Agilent Technologies).

organism: Homo sapiens

source_name: Adult human dermal fibroblasts-G

label_protocol: Labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit.

growth_protocol: For erythroblast expansion: 50% IMDM+50% Ham’s F12 with synthetic lipids, ITS supplement, BSA, ascorbic acid, glutamine, IL-3, SCF EPO, IGF-1 and dexamethasone. For CD34+ cells expansion: 50% IMDM+50% Ham’s F12 with synthetic lipids, ITS supplement, ascorbic acid, glutamine, IL-3, SCF, Fit3-L and TPO. For HDF-G: Medium 106 supplemented with Low Serum Growth Supplement, For HDF-K: 10% FCS-DMEM.

extract_protocol: Total RNA was isolated using RNeasy kit (QIAGEN) according to the manufacturer's protocol.

tag: gender

value: female

value: skin


title: Crick_SiPos_1

extract_protocol:
Nuclear RNA was isolated using PureLink RNA Micro Kit (Invitrogen #12183016) according to the manufacturer’s instructions.
Double stranded full-length cDNA was generated using the Ovation RNA-Seq System V2 (NuGen Technologies, Inc.). Following quantification on a Qubit 3.0 fluorometer (Thermo Fisher Scientific, Inc.), cDNA was fragmented to 200bp by acoustic shearing using Covaris E220 instrument (Covaris, Inc.) at standard settings. The fragmented cDNA was then normalized to 100ng, which was used for sequencing library preparation using the Ovation Ultralow System V2 1-96 protocol (NuGen Technologies, Inc.). A total of 8 PCR cycles were used for library amplification. The quality and quantity of the final libraries were assessed with TapeStation D1000 Assay (Agilent Technologies, Inc.). The libraries were then normalized to 2.5 nM, pooled and loaded onto a HiSeq4000 (Illumina, Inc.) to generate 75bp single-end reads.

value: Specific pathogen-free (SPF)

tag: animal facility

value: The Francic Crick Institute

value: small intestine (SI)


title: Crick_SiPos_3


title: Crick_SiPos_2


title: Crick_SiPos_4


title: Erythroblasts-rich fraction_rep2

description: Cells were prepared on the 8th day of culture.

source_name: Erythroblasts-rich fraction expanded from human cord blood, CB-2-2

value: cord blood


title: CD34(+)-rich fraction_rep1

source_name: CD34(+)-rich fraction expanded from human cord blood, CB-1

value: male


title: Human dermal fibroblasts_rep2

source_name: Adult human dermal fibroblasts-K


title: Erythroblasts-rich fraction_rep1

source_name: Erythroblasts-rich fraction expanded from human cord blood, CB-1


title: Neuron_AhrAgo_4


title: Crick_SiNeg_2


title: Erythroblasts-rich fraction_rep3

source_name: Erythroblasts-rich fraction expanded from human cord blood, CB-2-3


title: Crick_ColPos_3


title: Crick_ColNeg_4


title: Crick_SiNeg_1


title: Crick_ColPos_4


title: BTX642 Roots, 105 days old, Control, plot 19

city: Berkeley

first: Benjamin

middle: Jeremy

last: Cole

state: CA

address: 1, Cyclotron Road

institute: DOE-Joint Genome Institute

description:
root_normCounts.txt
0914167R19

data_processing:
Using BBDuk, raw reads were evaluated for artifact sequence by kmer matching (kmer=25), allowing 1 mismatch and detected artifact was trimmed from the 3'end of the reads.
RNA spike-in reads, PhiX reads and reads containing any Ns were removed.
Quality trimming was performed using the phred trimming method set at Q6.
Following trimming, reads under the length threshold were removed (minimum length 25 bases or 1/3 of the original read length - whichever is longer).
Filtered reads from each library were aligned to the reference genome (phytozome v3.1, supplemented with RTx430 and BTx642 SNP information) using HISAT version 2.1.0. featureCounts was used to generate the raw gene counts file using gff3 annotations. Only primary hits assigned to the reverse strand were included in the raw gene counts (-s 2 -p --primary options).
Genome_build: Sorghum bicolor v. 3.1 (JGI), supplemented with resequence data available in SRR4028151 (BTx642) or SRR4028129 (RTx430)
Supplementary_files_format_and_content: normalized counts for root and leaf tissues are provided separately as text files. The reference genome fasta files (SNP-corrected) are provided as fasta files.

molecule: polyA RNA

organism: Sorghum bicolor

source_name: Roots

extract_protocol:
Frozen root and leaf tissue were ground in a cryogenic Freezer Mill (SPEX SamplePrep 6875D, Metuchen NJ USA) for 2-3 cycles of 2-3 minutes, with 1 minute cooling in between. Samples were then stored at -80C. RNA was extracted using the QIAGEN miRNeasy mini kit (Cat. #AM217004) with modifications: 1 mL QIAzol (Cat) and 100 uL 10% Sarkosyl solution were added to 100 mg of frozen tissue and placed in a vortex shaker adapter for 5 minutes. To these, 200 uL chloroform was added, and the samples were then vortexed and incubated for 3 minutes at room temperature before centrifugation at 12,000 xg for 15 min at 4C. The aqueous phase was then transferred to a fresh tube, and ethanol was added to a final concentration of 60%. The remaining procedure was performed according to the manufacturer’s recommendations. DNA contamination was removed from each sample using the TURBO DNA-free kit, (Cat. # AM1907, Invitrogen) according to the manufacturer’s recommendations.
Stranded cDNA libraries were generated using the Illumina Truseq Stranded RNA LT kit. mRNA was purified from 1 ug of total RNA using magnetic beads containing poly-T oligos. mRNA was fragmented and reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis. The fragmented cDNA was treated with end-pair, A-tailing, adapter ligation, and 8 cycles of PCR. qPCR was used to determine the concentration of the libraries.

tag: watering regime

value: Control

tag: age (days)

tag: plot


title: BTX642 Roots, 119 days old, Control, plot 19

description:
root_normCounts.txt
0928169R19


title: BTX642 Roots, 105 days old, Control, plot 11

description:
root_normCounts.txt
0914167R11


title: Crick_ColPos_2

tag: tissue


title: BTX642 Roots, 84 days old, Control, plot 19

description:
root_normCounts.txt
0824164R19


title: BTX642 Roots, 91 days old, Control, plot 11

description:
root_normCounts.txt
0831165R11


title: BTX642 Roots, 91 days old, Control, plot 2

description:
root_normCounts.txt
0831165R02


title: BTX642 Roots, 91 days old, Control, plot 19

description:
root_normCounts.txt
0831165R19


title: Crick_ColNeg_2

tag: strain


title: Crick_SiNeg_4


title: Crick_SiNeg_3


title: BTX642 Roots, 98 days old, Control, plot 11

description:
root_normCounts.txt
0907166R11


title: Crick_ColNeg_1


title: Bern_SiPos_3

value: University of Bern


title: BTX642 Roots, 119 days old, Control, plot 2

description:
root_normCounts.txt
0928169R02


title: BTX642 Roots, 77 days old, Control, plot 2

description:
root_normCounts.txt
0817163R02


title: BTX642 Roots, 84 days old, Control, plot 11

description:
root_normCounts.txt
0824164R11


title: BTX642 Roots, 119 days old, Control, plot 11

description:
root_normCounts.txt
0928169R11


title: BTX642 Roots, 77 days old, Control, plot 11

description:
root_normCounts.txt
0817163R11


title: Crick_ColPos_1


title: Crick_ColNeg_3


title: Bern_SiPos_1


title: BTX642 Roots, 77 days old, Control, plot 19

description:
root_normCounts.txt
0817163R19


title: Bern_SiNeg_4


title: Bern_SiNeg_3


title: Bern_SiNeg_2


title: BTX642 Roots, 70 days old, Control, plot 11

description:
root_normCounts.txt
0810162R11


title: BTX642 Roots, 70 days old, Control, plot 2

description:
root_normCounts.txt
0810162R02


title: BTX642 Roots, 84 days old, Control, plot 2

description:
root_normCounts.txt
0824164R02


title: BTX642 Roots, 63 days old, Control, plot 11

description:
root_normCounts.txt
0803169R11


title: Bern_ColPos_3


title: Bern_ColPos_4


title: Bern_SiPos_4


title: BTX642 Roots, 63 days old, Control, plot 19

description:
root_normCounts.txt
0803169R19


title: BTX642 Roots, 63 days old, Control, plot 2

description:
root_normCounts.txt
0803169R02


title: BTX642 Roots, 56 days old, Control, plot 2

description:
root_normCounts.txt
0727168R02


title: Bern_ColPos_2


title: Bern_ColPos_1


title: Bern_ColNeg_4


title: Bern_SiPos_2


title: BTX642 Roots, 56 days old, Control, plot 19

description:
root_normCounts.txt
0727168R19


title: Bern_ColNeg_3


title: Bern_ColNeg_1


title: BTX642 Roots, 42 days old, Control, plot 2

description:
root_normCounts.txt
0713166R02


title: BTX642 Roots, 42 days old, Control, plot 19

description:
root_normCounts.txt
0713166R19


title: SPF_SiPos_4


title: SPF_SiPos_3


title: Bern_SiNeg_1


title: Bern_ColNeg_2


title: BTX642 Roots, 56 days old, Control, plot 11

description:
root_normCounts.txt
0727168R11


title: SPF_SiPos_1


title: SPF_SiNeg_4


title: SPF_SiNeg_3


title: BTX642 Roots, 28 days old, Control, plot 19

description:
root_normCounts.txt
0629164R19


title: SPF_SiNeg_1


title: SPF_SiNeg_2


title: BTX642 Roots, 35 days old, Control, plot 19

description:
root_normCounts.txt
0706165R19


title: BTX642 Roots, 49 days old, Control, plot 11

description:
root_normCounts.txt
0720167R11


title: SPF_ColPos_3


title: BTX642 Roots, 21 days old, Control, plot 2

description:
root_normCounts.txt
0622162R02


title: BTX642 Roots, 28 days old, Control, plot 2

description:
root_normCounts.txt
0629164R02


title: BTX642 Roots, 28 days old, Control, plot 11

description:
root_normCounts.txt
0629164R11


title: BTX642 Roots, 21 days old, Control, plot 19

description:
root_normCounts.txt
0622162R19


title: BTX642 Roots, 21 days old, Control, plot 11

description:
root_normCounts.txt
0622162R11


title: SPF_ColPos_2


title: SPF_ColPos_4


title: BTX642 Roots, 42 days old, Control, plot 11

description:
root_normCounts.txt
0713166R11


title: SPF_ColPos_1


title: SPF_ColNeg_4


title: BTX642 Roots, 14 days old, Control, plot 2

description:
root_normCounts.txt
0615163R02


title: BTX642 Roots, 35 days old, Control, plot 2

description:
root_normCounts.txt
0706165R02


title: SPF_ColNeg_3


title: BTX642 Roots, 70 days old, Control, plot 19

description:
root_normCounts.txt
0810162R19


title: SPF_SiPos_2


title: BTX642 Roots, 14 days old, Control, plot 11

description:
root_normCounts.txt
0615163R11


title: BTX642 Roots, 14 days old, Control, plot 19

description:
root_normCounts.txt
0615163R19


title: BTX642 Roots, 35 days old, Control, plot 11

description:
root_normCounts.txt
0706165R11


title: BTX642 Roots, 119 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0928169R21

value: Postflowering drought stress


title: SPF_ColNeg_2


title: BTX642 Roots, 119 days old, Postflowering drought stress, plot 15

description:
root_normCounts.txt
0928169R15


title: BTX642 Roots, 119 days old, Postflowering drought stress, plot 4

description:
root_normCounts.txt
0928169R04


title: BTX642 Roots, 105 days old, Postflowering drought stress, plot 4

description:
root_normCounts.txt
0914167R04


title: GF_SiPos_2

value: Germ-free (GF)


title: BTX642 Roots, 105 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0914167R21


title: GF_SiPos_1


title: GF_SiNeg_3


title: BTX642 Roots, 98 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0907166R21


title: BTX642 Roots, 91 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0831165R21


title: GF_SiPos_3


title: GF_SiNeg_2


title: GF_ColPos_3


title: BTX642 Roots, 105 days old, Postflowering drought stress, plot 15

description:
root_normCounts.txt
0914167R15


title: GF_ColPos_2


title: BTX642 Roots, 91 days old, Postflowering drought stress, plot 4

description:
root_normCounts.txt
0831165R04


title: GF_SiNeg_1


title: BTX642 Roots, 84 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0824164R21


title: BTX642 Roots, 91 days old, Postflowering drought stress, plot 15

description:
root_normCounts.txt
0831165R15


title: GF_ColPos_1


title: BTX642 Roots, 77 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0817163R21


title: BTX642 Roots, 77 days old, Postflowering drought stress, plot 4

description:
root_normCounts.txt
0817163R04


title: GF_ColNeg_3


title: BTX642 Roots, 77 days old, Postflowering drought stress, plot 15

description:
root_normCounts.txt
0817163R15


title: GF_ColNeg_1


title: BTX642 Roots, 70 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0810162R21


title: BTX642 Roots, 112 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0921168R21


title: BTX642 Roots, 70 days old, Postflowering drought stress, plot 15

description:
root_normCounts.txt
0810162R15


title: GF_ColNeg_2


title: Kidney2

city: South San Francisco

first: Nicholas

last: Bernstein

address: 1130 Veterans Blvd

institute: Calico labs

description:
polyA RNA
Well 2 from 10x run, gene expression measurements, from 2 dissociated mouse kidneys that were FACs sorted

data_processing:
Basecalling with IlluminaBCL2FASTQ (versionv2.20.0.422
Gene expression quantification with Kallisto bus (version 0.46.0) and BUStools correct (version 0.39.2)
CMO quantification was done with Kite; https://github.com/pachterlab/kite and CMO groups were grouped according to
We removed cells with fewer than 100 genes and 2,000 UMI counts. We removed cells with greater than 60% UMIs coming from mitochondrial genes
Doublet identication was done using Solo and HashSolo which can be found at https://github.com/calico/solo
Genome_build: mm10 Ensembl v96 transcriptome
Supplementary_files_format_and_content: Cell-Gene expression matrices and Cell-CMO count matrices are provided in matrix market format. Doublet and cell type information from solo, hashsolo and scNym are provided in a csv file.

growth_protocol: Mice were maintained on a 12 hour light/dark cycle with ad libitum feeding.

extract_protocol:
Kidneys were harvested and stored in DMEM on ice. Kidneys were dissociated with 0.2 mg/mLof Liberase TM in DMEM at37◦C 800 rpm for 45 minutes (Thermomixer C). Aliquots were taken and visualized under the microscope until tissue was completely dissociated. Liberase TM was inactivated with DMEM+10% fetal bovine serum (FBS) and dissociated cells were filtered through a100μm and 40μm filter. Dissociated cells were then spun down at 200×g for 5 minutes at 4◦C and resuspended in PBS+1% BSA.
We loaded a total of 80,000 sorted cells into two wells on the 10x Chromium system (40,000 per well; 10X Genomics). We generated barcoded cDNA libraries using the Chromium Single Cell 3’ Library Construction Kit (V3; 10XGenomics).


title: Kidney2ST

description:
CMO
Well 2 from 10x run, cholestorol modified oligos (CMO) measurements to experimentally identify doublets, from 2 dissociated mouse kidneys that were FACs sorted


title: Kidney1ST

description:
CMO
Well 1 from 10x run, cholestorol modified oligos (CMO) measurements to experimentally identify doublets, from 2 dissociated mouse kidneys that were FACs sorted


title: Kidney1

description:
polyA RNA
Well 1 from 10x run, gene expression measurements, from 2 dissociated mouse kidneys that were FACs sorted


title: BTX642 Roots, 70 days old, Postflowering drought stress, plot 4

description:
root_normCounts.txt
0810162R04


title: BTX642 Roots, 63 days old, Postflowering drought stress, plot 15

description:
root_normCounts.txt
0803169R15


title: KPB25Luv-Nottreated

data_processing:
The Cell Ranger Single Cell Software Suite, version 1.3 was used for de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. Reads were mapped to the mm10 genome.
Specific details and instructions to run Cell Ranger can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Genome_build: mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Mammary tumor

growth_protocol: Tumor cells were orthotopically injected to the number 4 mammary gland. Tumors were allowed to grow to a diameter of 5mm and then randomly assigned to treatment.

extract_protocol:
Single cell suspensions were obtained using Miltenyi tumor dissociation kits (130-096-730). Single cell suspensions were input to a 10x Genomics Chromium machine to establish single-cell gel beads in emulsion (GEMs) for directed retrieval of approximately 5000-10000 cells
Single-cell RNA-Seq libraries were primed using the following Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics). Protocols were performed as directed in the Single Cell 3’ Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A)
Libraries were sequenced on an Illumina HiSeq 4000 as 2 × 150 paired-end reads.

treatment_protocol: anti-PD1 (10mg/kg) + aCTLA4 (100ug) therapy biweekly; Therapy began at tumor diameter of 5mm. Samples collected after 7 days therapy.

value: FVB/NJ

tag: Sex


title: T11-Apobec-Nottreated

value: Balbc


title: KPB25Luv-7daytreated

value: aPD1/aCTLA4 therapy


title: T11-Apobec-7daytreated


title: SPF_ColNeg_1

value: colon

value: non-neuronal

value: Nuclear mRNA


title: BTX642 Roots, 119 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0928169R14

value: Preflowering drought stress


title: BTX642 Roots, 119 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0928169R17


title: BTX642 Roots, 63 days old, Postflowering drought stress, plot 4

description:
root_normCounts.txt
0803169R04


title: BTX642 Roots, 119 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0928169R06


title: BTX642 Roots, 112 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0921168R06


title: BTX642 Roots, 105 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0914167R17


title: BTX642 Roots, 98 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0907166R06


title: spinal_cord_ethanol_no_injection_wild-type_Day_8_rep3

first: Diana

middle: M

last: Bautista

address: 142 Life Sciences Addition

department: Molecular and Cellular Biology

institute: UC Berkeley

data_processing:
Illumina Casava2.19 software used for basecalling.
readmapping was performed using Tophat2 and Bowtie2 as follows: "tophat -o --max-multihits 1 -G  --no-novel-juncs --no-novel-indels", with fastq as input and mm10 genome and .gtf provided
abundance measurements were collected using "htseq-count -s no -m intersection-strict" with .bamfile as input and mm10 .gtf provided
Genome_build: mm10
Supplementary_files_format_and_content: read counts/abundance files were generated using HTSeq-count and are provided as text files

extract_protocol:
RNAzol RT large RNA extraction of homogenized tissues according to manufacturer's protocol (Sigma)
Libraries were prepared using standard Illumina protocols

treatment_protocol: Mice were treated once-daily with 0.2 mM MC903 (Tocris) dissolved in 100% Ethanol (-20C) or Ethanol vehicle (20 µL).

tag: developmental stage

value: adult

value: ethanol

value: wild-type

tag: time point


title: spinal_cord_ethanol_no_injection_wild-type_Day_8_rep4


title: spinal_cord_ethanol_no_injection_wild-type_Day_8_rep2


title: spinal_cord_ethanol_no_injection_wild-type_Day_8_rep1


title: BTX642 Roots, 105 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0914167R14


title: spinal_cord_ethanol_no_injection_wild-type_Day_8_rep5


title: spinal_cord_mc903_no_injection_wild-type_Day_8_rep3


title: BTX642 Roots, 91 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0831165R17


title: BTX642 Roots, 91 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0831165R06


title: spinal_cord_mc903_no_injection_wild-type_Day_8_rep4


title: spinal_cord_mc903_no_injection_wild-type_Day_8_rep1


title: spinal_cord_mc903_no_injection_wild-type_Day_8_rep2


title: BTX642 Roots, 91 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0831165R14


title: BTX642 Roots, 84 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0824164R17


title: BTX642 Roots, 84 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0824164R14


title: BTX642 Roots, 63 days old, Postflowering drought stress, plot 21

description:
root_normCounts.txt
0803169R21


title: BTX642 Roots, 84 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0824164R06


title: spinal_cord_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep5


title: spinal_cord_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep4


title: BTX642 Roots, 77 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0817163R17


title: spinal_cord_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep6


title: BTX642 Roots, 77 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0817163R06


title: BTX642 Roots, 70 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0810162R06


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep5


title: BTX642 Roots, 70 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0810162R17


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep6


title: BTX642 Roots, 77 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0817163R14


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep7


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep3


title: BTX642 Roots, 70 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0810162R14


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep2


title: spinal_cord_ethanol_PBS_wild-type_Day_8_rep2

value: PBS


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep4


title: BTX642 Roots, 63 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0803169R17


title: BTX642 Roots, 63 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0803169R06


title: spinal_cord_mc903_PBS_wild-type_Day_8_rep2


title: spinal_cord_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep3


title: BTX642 Roots, 56 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0727168R06


title: BTX642 Roots, 63 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0803169R14


title: BTX642 Roots, 56 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0727168R17


title: spinal_cord_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep2


title: spinal_cord_ethanol_PBS_wild-type_Day_8_rep1


title: BTX642 Roots, 49 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0720167R06


title: spinal_cord_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep1


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep8


title: BTX642 Roots, 42 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0713166R14


title: BTX642 Roots, 42 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0713166R06


title: BTX642 Roots, 35 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0706165R17


title: spinal_cord_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep1


title: BTX642 Roots, 42 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0713166R17


title: BTX642 Roots, 35 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0706165R06


title: BTX642 Roots, 35 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0706165R14


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_12_rep2


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_12_rep1


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_12_rep4


title: spinal_cord_mc903_PBS_wild-type_Day_8_rep1


title: BTX642 Roots, 28 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0629164R14


title: BTX642 Roots, 28 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0629164R17


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_12_rep3


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_12_rep5


title: BTX642 Roots, 21 days old, Preflowering drought stress, plot 17

description:
root_normCounts.txt
0622162R17


title: BTX642 Roots, 28 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0629164R06


title: BTX642 Roots, 21 days old, Preflowering drought stress, plot 14

description:
root_normCounts.txt
0622162R14


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_12_rep2


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_12_rep4


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_12_rep1


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_12_rep3


title: skin_ethanol_no_injection_wild-type_Day_12_rep5

source_name: skin


title: skin_ethanol_no_injection_wild-type_Day_12_rep4


title: BTX642 Roots, 21 days old, Preflowering drought stress, plot 6

description:
root_normCounts.txt
0622162R06


title: RTX430 Roots, 119 days old, Control, plot 12

description:
root_normCounts.txt
0928169R12


title: RTX430 Roots, 112 days old, Control, plot 12

description:
root_normCounts.txt
0921168R12


title: RTX430 Roots, 119 days old, Control, plot 20

description:
root_normCounts.txt
0928169R20


title: RTX430 Roots, 119 days old, Control, plot 1

description:
root_normCounts.txt
0928169R01


title: RTX430 Roots, 105 days old, Control, plot 1

description:
root_normCounts.txt
0914167R01


title: skin_ethanol_no_injection_wild-type_Day_12_rep3


title: skin_ethanol_no_injection_wild-type_Day_12_rep1


title: skin_mc903_no_injection_wild-type_Day_12_rep4


title: RTX430 Roots, 105 days old, Control, plot 12

description:
root_normCounts.txt
0914167R12


title: skin_mc903_no_injection_wild-type_Day_12_rep3


title: skin_mc903_no_injection_wild-type_Day_12_rep1


title: RTX430 Roots, 91 days old, Control, plot 1

description:
root_normCounts.txt
0831165R01


title: RTX430 Roots, 98 days old, Control, plot 12

description:
root_normCounts.txt
0907166R12


title: RTX430 Roots, 91 days old, Control, plot 12

description:
root_normCounts.txt
0831165R12


title: RTX430 Roots, 91 days old, Control, plot 20

description:
root_normCounts.txt
0831165R20


title: trigeminal_ganglion_ethanol_no_injection_TSLPR.KO_Day_12_rep4


title: skin_mc903_no_injection_wild-type_Day_12_rep2


title: trigeminal_ganglion_ethanol_no_injection_TSLPR.KO_Day_12_rep2


title: trigeminal_ganglion_ethanol_no_injection_TSLPR.KO_Day_12_rep3


title: trigeminal_ganglion_mc903_no_injection_TSLPR.KO_Day_12_rep3


title: trigeminal_ganglion_mc903_no_injection_TSLPR.KO_Day_12_rep4


title: RTX430 Roots, 77 days old, Control, plot 1

description:
root_normCounts.txt
0817163R01


title: RTX430 Roots, 77 days old, Control, plot 20

description:
root_normCounts.txt
0817163R20


title: RTX430 Roots, 77 days old, Control, plot 12

description:
root_normCounts.txt
0817163R12


title: trigeminal_ganglion_ethanol_no_injection_TSLPR.KO_Day_12_rep1


title: trigeminal_ganglion_mc903_no_injection_TSLPR.KO_Day_12_rep2


title: RTX430 Roots, 105 days old, Control, plot 20

description:
root_normCounts.txt
0914167R20


title: RTX430 Roots, 70 days old, Control, plot 12

description:
root_normCounts.txt
0810162R12


title: RTX430 Roots, 84 days old, Control, plot 12

description:
root_normCounts.txt
0824164R12


title: trigeminal_ganglion_mc903_no_injection_TSLPR.KO_Day_12_rep1


title: skin_ethanol_no_injection_TSLPR.KO_Day_12_rep3


title: skin_ethanol_no_injection_wild-type_Day_12_rep2


title: RTX430 Roots, 63 days old, Control, plot 12

description:
root_normCounts.txt
0803169R12


title: skin_mc903_no_injection_TSLPR.KO_Day_12_rep4


title: RTX430 Roots, 70 days old, Control, plot 1

description:
root_normCounts.txt
0810162R01


title: RTX430 Roots, 63 days old, Control, plot 20

description:
root_normCounts.txt
0803169R20


title: skin_ethanol_no_injection_TSLPR.KO_Day_12_rep1


title: RTX430 Roots, 56 days old, Control, plot 1

description:
root_normCounts.txt
0727168R01


title: skin_ethanol_no_injection_TSLPR.KO_Day_12_rep2


title: RTX430 Roots, 56 days old, Control, plot 20

description:
root_normCounts.txt
0727168R20


title: skin_mc903_no_injection_TSLPR.KO_Day_12_rep3


title: skin_mc903_no_injection_TSLPR.KO_Day_12_rep1


title: skin_ethanol_PBS_wild-type_Day_8_rep3


title: RTX430 Roots, 49 days old, Control, plot 12

description:
root_normCounts.txt
0720167R12


title: RTX430 Roots, 56 days old, Control, plot 12

description:
root_normCounts.txt
0727168R12


title: RTX430 Roots, 63 days old, Control, plot 1

description:
root_normCounts.txt
0803169R01


title: RTX430 Roots, 70 days old, Control, plot 20

description:
root_normCounts.txt
0810162R20


title: RTX430 Roots, 42 days old, Control, plot 1

description:
root_normCounts.txt
0713166R01


title: RTX430 Roots, 42 days old, Control, plot 20

description:
root_normCounts.txt
0713166R20


title: RTX430 Roots, 35 days old, Control, plot 12

description:
root_normCounts.txt
0706165R12


title: skin_mc903_PBS_wild-type_Day_8_rep2


title: skin_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep3


title: RTX430 Roots, 42 days old, Control, plot 12

description:
root_normCounts.txt
0713166R12


title: skin_mc903_PBS_wild-type_Day_8_rep1


title: RTX430 Roots, 28 days old, Control, plot 20

description:
root_normCounts.txt
0629164R20


title: skin_ethanol_PBS_wild-type_Day_8_rep1


title: skin_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep2


title: skin_ethanol_PBS_wild-type_Day_8_rep2


title: RTX430 Roots, 28 days old, Control, plot 1

description:
root_normCounts.txt
0629164R01


title: RTX430 Roots, 35 days old, Control, plot 1

description:
root_normCounts.txt
0706165R01


title: skin_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep1


title: RTX430 Roots, 21 days old, Control, plot 1

description:
root_normCounts.txt
0622162R01


title: skin_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep4


title: RTX430 Roots, 21 days old, Control, plot 20

description:
root_normCounts.txt
0622162R20


title: skin_mc903_no_injection_TSLPR.KO_Day_12_rep2


title: skin_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep3


title: RTX430 Roots, 21 days old, Control, plot 12

description:
root_normCounts.txt
0622162R12


title: skin_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep2


title: skin_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep4


title: RTX430 Roots, 14 days old, Control, plot 1

description:
root_normCounts.txt
0615163R01


title: RTX430 Roots, 14 days old, Control, plot 20

description:
root_normCounts.txt
0615163R20


title: trigeminal_ganglion_ethanol_PBS_wild-type_Day_8_rep3


title: RTX430 Roots, 14 days old, Control, plot 12

description:
root_normCounts.txt
0615163R12


title: RTX430 Roots, 119 days old, Postflowering drought stress, plot 3

description:
root_normCounts.txt
0928169R03


title: RTX430 Roots, 119 days old, Postflowering drought stress, plot 16

description:
root_normCounts.txt
0928169R16


title: RTX430 Roots, 119 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0928169R22


title: trigeminal_ganglion_mc903_PBS_wild-type_Day_8_rep4


title: trigeminal_ganglion_ethanol_PBS_wild-type_Day_8_rep2


title: trigeminal_ganglion_mc903_PBS_wild-type_Day_8_rep1


title: trigeminal_ganglion_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep4


title: trigeminal_ganglion_mc903_PBS_wild-type_Day_8_rep3


title: RTX430 Roots, 105 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0914167R22


title: RTX430 Roots, 28 days old, Control, plot 12

description:
root_normCounts.txt
0629164R12


title: trigeminal_ganglion_mc903_PBS_wild-type_Day_8_rep2


title: RTX430 Roots, 105 days old, Postflowering drought stress, plot 16

description:
root_normCounts.txt
0914167R16


title: RTX430 Roots, 112 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0921168R22


title: RTX430 Roots, 91 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0831165R22


title: RTX430 Roots, 98 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0907166R22


title: RTX430 Roots, 105 days old, Postflowering drought stress, plot 3

description:
root_normCounts.txt
0914167R03


title: trigeminal_ganglion_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep2


title: RTX430 Roots, 91 days old, Postflowering drought stress, plot 16

description:
root_normCounts.txt
0831165R16


title: trigeminal_ganglion_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep1


title: trigeminal_ganglion_ethanol_250.µg.anti-Gr1_wild-type_Day_8_rep3


title: skin_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep1


title: trigeminal_ganglion_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep3


title: trigeminal_ganglion_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep2


title: RTX430 Roots, 91 days old, Postflowering drought stress, plot 3

description:
root_normCounts.txt
0831165R03


title: trigeminal_ganglion_ethanol_PBS_wild-type_Day_8_rep1


title: RTX430 Roots, 77 days old, Postflowering drought stress, plot 16

description:
root_normCounts.txt
0817163R16


title: RTX430 Roots, 77 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0817163R22


title: trigeminal_ganglion_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep1


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_8_rep3


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_8_rep1


title: RTX430 Roots, 70 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0810162R22


title: RTX430 Roots, 70 days old, Postflowering drought stress, plot 3

description:
root_normCounts.txt
0810162R03


title: RTX430 Roots, 63 days old, Postflowering drought stress, plot 16

description:
root_normCounts.txt
0803169R16


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_8_rep3


title: RTX430 Roots, 63 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0803169R22


title: RTX430 Roots, 70 days old, Postflowering drought stress, plot 16

description:
root_normCounts.txt
0810162R16


title: RTX430 Roots, 63 days old, Postflowering drought stress, plot 3

description:
root_normCounts.txt
0803169R03


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_8_rep2


title: RTX430 Roots, 77 days old, Postflowering drought stress, plot 3

description:
root_normCounts.txt
0817163R03


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_8_rep1


title: trigeminal_ganglion_mc903_250.µg.anti-Gr1_wild-type_Day_8_rep4


title: RTX430 Roots, 119 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0928169R13


title: trigeminal_ganglion_mc903_no_injection_TSLPR.KO_Day_8_rep1


title: trigeminal_ganglion_mc903_no_injection_TSLPR.KO_Day_8_rep2


title: RTX430 Roots, 119 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0928169R18


title: RTX430 Roots, 112 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0921168R05


title: RTX430 Roots, 84 days old, Postflowering drought stress, plot 22

description:
root_normCounts.txt
0824164R22


title: RTX430 Roots, 105 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0914167R13


title: skin_ethanol_no_injection_wild-type_Day_8_rep3


title: skin_ethanol_no_injection_wild-type_Day_8_rep1


title: RTX430 Roots, 105 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0914167R05


title: RTX430 Roots, 91 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0831165R18


title: RTX430 Roots, 119 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0928169R05


title: trigeminal_ganglion_ethanol_no_injection_TSLPR.KO_Day_8_rep1


title: RTX430 Roots, 91 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0831165R05


title: skin_ethanol_no_injection_TSLPR.KO_Day_8_rep1


title: skin_mc903_no_injection_TSLPR.KO_Day_8_rep3


title: RTX430 Roots, 84 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0824164R05


title: skin_mc903_no_injection_TSLPR.KO_Day_8_rep2


title: RTX430 Roots, 77 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0817163R05


title: skin_ethanol_no_injection_wild-type_Day_8_rep2


title: RTX430 Roots, 84 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0824164R18


title: skin_ethanol_no_injection_BLT1.KO_Day_8_rep3


title: RTX430 Roots, 91 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0831165R13


title: skin_mc903_no_injection_BLT1.KO_Day_8_rep3


title: RTX430 Roots, 77 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0817163R13


title: skin_mc903_no_injection_BLT1.KO_Day_8_rep2


title: skin_mc903_no_injection_TSLPR.KO_Day_8_rep1


title: skin_mc903_no_injection_wild-type_Day_8_rep2


title: RTX430 Roots, 70 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0810162R05


title: RTX430 Roots, 98 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0907166R05


title: skin_mc903_no_injection_wild-type_Day_8_rep1


title: skin_mc903_no_injection_BLT1.KO_Day_8_rep1


title: skin_ethanol_no_injection_BLT1.KO_Day_8_rep1


title: skin_ethanol_no_injection_TSLPR.KO_Day_8_rep2


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_1_rep4


title: RTX430 Roots, 77 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0817163R18


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_1_rep3


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_8_rep2


title: RTX430 Roots, 70 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0810162R18


title: skin_ethanol_no_injection_BLT1.KO_Day_8_rep2


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_1_rep2


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_1_rep1


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_1_rep3


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_1_rep4


title: RTX430 Roots, 63 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0803169R18


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_1_rep1


title: RTX430 Roots, 63 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0803169R05


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_1_rep2


title: RTX430 Roots, 70 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0810162R13


title: RTX430 Roots, 56 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0727168R13


title: RTX430 Roots, 56 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0727168R18


title: RTX430 Roots, 56 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0727168R05


title: RTX430 Roots, 63 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0803169R13


title: skin_ethanol_no_injection_wild-type_Day_1_rep4


title: RTX430 Roots, 42 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0713166R05


title: skin_ethanol_no_injection_wild-type_Day_1_rep3


title: RTX430 Roots, 35 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0706165R05


title: skin_ethanol_no_injection_wild-type_Day_1_rep2


title: skin_ethanol_no_injection_wild-type_Day_1_rep1


title: skin_mc903_no_injection_wild-type_Day_1_rep3


title: skin_mc903_no_injection_wild-type_Day_1_rep4


title: RTX430 Roots, 49 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0720167R05


title: RTX430 Roots, 28 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0629164R13


title: RTX430 Roots, 35 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0706165R13


title: RTX430 Roots, 42 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0713166R18


title: RTX430 Roots, 28 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0629164R05


title: skin_mc903_no_injection_wild-type_Day_1_rep2


title: RTX430 Roots, 42 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0713166R13


title: RTX430 Roots, 21 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0622162R18


title: skin_mc903_no_injection_wild-type_Day_1_rep1


title: BTX642 Leaves, 105 days old, Control, plot 11

description:
leaf_normCounts.txt
0914167L11

source_name: Leaves


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_8_rep2 [DBRH_TG2_S34]


title: BTX642 Leaves, 119 days old, Control, plot 2

description:
leaf_normCounts.txt
0928169L02


title: RTX430 Roots, 28 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0629164R18


title: RTX430 Roots, 21 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0622162R13


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_8_rep1 [DBRH_TG3_S35]


title: skin_mc903_no_injection_wild-type_Day_8_rep1 [DBRH_skin4_S30]


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_8_rep2 [DBRH_TG6_7_S36]


title: skin_ethanol_no_injection_wild-type_Day_8_rep2 [DBRH_skin6_S31]


title: RTX430 Roots, 35 days old, Preflowering drought stress, plot 18

description:
root_normCounts.txt
0706165R18


title: skin_ethanol_no_injection_wild-type_Day_8_rep3 [DBRH_skin7_S32]


title: RTX430 Roots, 21 days old, Preflowering drought stress, plot 5

description:
root_normCounts.txt
0622162R05


title: skin_ethanol_no_injection_wild-type_Day_8_rep3 [DBRH_skin3_S29]


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_8_rep1 [DBRH_TG1_S33]


title: BTX642 Leaves, 105 days old, Control, plot 2

description:
leaf_normCounts.txt
0914167L02


title: BTX642 Leaves, 105 days old, Control, plot 19

description:
leaf_normCounts.txt
0914167L19


title: BTX642 Leaves, 119 days old, Control, plot 19

description:
root_normCounts.txt
0928169L19


title: skin_mc903_no_injection_wild-type_Day_8_rep2 [DBRH_skin2_S28]


title: BTX642 Leaves, 98 days old, Control, plot 11

description:
leaf_normCounts.txt
0907166L11


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_5_rep3


title: BTX642 Leaves, 91 days old, Control, plot 11

description:
leaf_normCounts.txt
0831165L11


title: BTX642 Leaves, 119 days old, Control, plot 11

description:
leaf_normCounts.txt
0928169L11


title: BTX642 Leaves, 91 days old, Control, plot 2

description:
leaf_normCounts.txt
0831165L02


title: skin_mc903_no_injection_wild-type_Day_8_rep1 [DBRH_skin1_S27]


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_5_rep1


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_5_rep2


title: BTX642 Leaves, 84 days old, Control, plot 11

description:
leaf_normCounts.txt
0824164L11


title: BTX642 Leaves, 84 days old, Control, plot 19

description:
leaf_normCounts.txt
0824164L19


title: BTX642 Leaves, 84 days old, Control, plot 2

description:
leaf_normCounts.txt
0824164L02


title: BTX642 Leaves, 91 days old, Control, plot 19

description:
leaf_normCounts.txt
0831165L19


title: BTX642 Leaves, 77 days old, Control, plot 19

description:
leaf_normCounts.txt
0817163L19


title: BTX642 Leaves, 77 days old, Control, plot 11

description:
leaf_normCounts.txt
0817163L11


title: BTX642 Leaves, 77 days old, Control, plot 2

description:
leaf_normCounts.txt
0817163L02


title: skin_ethanol_no_injection_wild-type_Day_5_rep3


title: skin_ethanol_no_injection_wild-type_Day_5_rep2


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_5_rep1


title: BTX642 Leaves, 70 days old, Control, plot 11

description:
leaf_normCounts.txt
0810162L11


title: skin_mc903_no_injection_wild-type_Day_5_rep1


title: skin_mc903_no_injection_wild-type_Day_5_rep3


title: BTX642 Leaves, 70 days old, Control, plot 2

description:
leaf_normCounts.txt
0810162L02


title: BTX642 Leaves, 63 days old, Control, plot 2

description:
leaf_normCounts.txt
0803169L02


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_5_rep2


title: skin_mc903_no_injection_wild-type_Day_5_rep2


title: skin_ethanol_no_injection_wild-type_Day_5_rep1


title: BTX642 Leaves, 70 days old, Control, plot 19

description:
leaf_normCounts.txt
0810162L19


title: BTX642 Leaves, 63 days old, Control, plot 11

description:
leaf_normCounts.txt
0803169L11


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_2_rep2


title: BTX642 Leaves, 63 days old, Control, plot 19

description:
leaf_normCounts.txt
0803169L19


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_2_rep2


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_5_rep3


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_2_rep1


title: BTX642 Leaves, 56 days old, Control, plot 2

description:
leaf_normCounts.txt
0727168L02


title: BTX642 Leaves, 49 days old, Control, plot 11

description:
leaf_normCounts.txt
0720167L11


title: BTX642 Leaves, 56 days old, Control, plot 19

description:
leaf_normCounts.txt
0727168L19


title: BTX642 Leaves, 56 days old, Control, plot 11

description:
leaf_normCounts.txt
0727168L11


title: trigeminal_ganglion_ethanol_no_injection_wild-type_Day_2_rep1


title: BTX642 Leaves, 42 days old, Control, plot 2

description:
leaf_normCounts.txt
0713166L02


title: BTX642 Leaves, 42 days old, Control, plot 19

description:
leaf_normCounts.txt
0713166L19


title: skin_mc903_no_injection_wild-type_Day_2_rep2


title: skin_ethanol_no_injection_wild-type_Day_2_rep2


title: BTX642 Leaves, 35 days old, Control, plot 11

description:
leaf_normCounts.txt
0706165L11


title: BTX642 Leaves, 35 days old, Control, plot 19

description:
leaf_normCounts.txt
0706165L19


title: skin_mc903_no_injection_wild-type_Day_2_rep3


title: BTX642 Leaves, 28 days old, Control, plot 19

description:
leaf_normCounts.txt
0629164L19


title: skin_ethanol_no_injection_wild-type_Day_2_rep1


title: trigeminal_ganglion_mc903_no_injection_wild-type_Day_2_rep3


title: trigeminal_ganglion_ethanol_no_injection_TSLPR.KO_Day_8_rep2


title: skin_mc903_no_injection_wild-type_Day_2_rep1


title: BTX642 Leaves, 21 days old, Control, plot 19

description:
leaf_normCounts.txt
0622162L19


title: BTX642 Leaves, 21 days old, Control, plot 11

description:
leaf_normCounts.txt
0622162L11


title: brp02

city: Lawrence

first: Clinton

middle: Allen

last: Rice

state: Kansas

address: 1200 Sunnyside Ave

department: Molecular Biosciences

institute: University of Kansas

data_processing:
The quality of the raw RNAseq reads was visually confirmed using FastQC (version 0.11.5), and both low quality data and adaptor sequences were removed using Trimmomatic (version 0.36).
Filtered reads were mapped to the D. melanogaster reference genome (Release 5.3) using TopHat (version 2.1.1) Default parameters were employed, with the addition of the "--no-novel-juncs" flag to use the gene annotation as provided, and the "--library-type fr-firststrand" flag since the RNAseq data derives from the Illumina TruSeq stranded mRNA kit.
Genotypes were compared, and differentially-expressed genes were identified using the Cufflinks pipeline (version 2.2.1, [27-29]). Specifically, we employed the "cuffquant" and "cuffdiff" routines using default paramaters, adding the "-b" flag to run a bias correction algorithm that improves expression estimates.
Genome_build: Drosophila melanogaster Release 5.3
Supplementary_files_format_and_content: Cufflinks output

organism: Drosophila melanogaster

source_name: Leg imaginal discs

extract_protocol:
Leg imaginal discs were dissected from larvae and prepupae in PBS, and RNA was isolated using Trizol reagent and purified over RNAeasy columns (Qiagen, Valencia, CA). ~1 ug of each sample was polyA selected, stranded, and library prepared using the TruSeq stranded mRNA kit (Illumina, San Diego, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: white prepupa (0 hrs)

value: leg imaginal discs


title: wPP01


title: wPP03


title: wL01

value: third instar larva (-18 hrs)


title: wPP02


title: wL02


title: brp03


title: BTX642 Leaves, 21 days old, Control, plot 2

description:
leaf_normCounts.txt
0622162L02

value: Control


title: wL03


title: BTX642 Leaves, 28 days old, Control, plot 2

description:
leaf_normCounts.txt
0629164L02


title: BTX642 Leaves, 35 days old, Control, plot 2

description:
leaf_normCounts.txt
0706165L02


title: BTX642 Leaves, 42 days old, Control, plot 11

description:
leaf_normCounts.txt
0713166L11


title: BTX642 Leaves, 14 days old, Control, plot 2

description:
leaf_normCounts.txt
0615163L02


title: brp01


title: BTX642 Leaves, 14 days old, Control, plot 19

description:
leaf_normCounts.txt
0615163L19


title: BTX642 Leaves, 14 days old, Control, plot 11

description:
leaf_normCounts.txt
0615163L11


title: stroke_2

city: Nanning

first: shenghua

last: Li

state: China

address: The First Affiliated Hospital of Guangxi Medical University

country: China

description:
Annotated_lncRNA_FPKM.txt
mRNA_FPKM.txt
Novel_lncRNA_FPKM.txt
Transcript_FPKM.txt
TUCP_FPKM.txt

data_processing:
sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina Hiseq 2500 platform and 125 bp paired-end reads were generated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using HISAT2 v2.0.4 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default.
The mapped reads of each sample were assembled by StringTie (v1.3.3) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
StringTie (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding transcripts in each sample (Mihaela Pertea et al. 2016). FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: blood

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: ethnicity

value: Han population

value: blood

tag: time

value: within three days of onset


title: BTX642 Leaves, 119 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0928169L21

tag: genotype

value: Postflowering drought stress


title: stroke_1

institute: The First Affiliated Hospital of Guangxi Medical University


title: BTX642 Leaves, 119 days old, Postflowering drought stress, plot 15

description:
leaf_normCounts.txt
0928169L15


title: BTX642 Leaves, 119 days old, Postflowering drought stress, plot 4

description:
leaf_normCounts.txt
0928169L04


title: ctr_3


title: stroke_3


title: BTX642 Leaves, 105 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0914167L21


title: ctr_1


title: DBJS_SLIGRL_5

data_processing:
Sequences were trimmed using Trimmomatic
Reads were mapped using Tophat2 to hg19 genome and gtf
Abundance counts were determined using htseq-union
Genome_build: hg19
Supplementary_files_format_and_content: htseq-count output file

source_name: Normal Human Epithelial Keratinocytes (Promocell, juvenile male foreskin, single donor)

growth_protocol: Cells were cultured according to suppliers instructions (Promocel C-12001)

extract_protocol:
RNA was extracted using Qiagen RNeasy Miniprep kit according to manufacturer's instructions
Libraries were made using standard Illumina protocols

treatment_protocol: Cells were treated with 100 µM SLIGRL (Tocris) or 0.1% DMSO vehicle for three hours at room temperature.

tag: cell type

value: NHEK

tag: passage

value: SLIGRL

value: juvenile


title: BTX642 Leaves, 105 days old, Postflowering drought stress, plot 15

description:
leaf_normCounts.txt
0914167L15


title: ctr_2


title: BTX642 Leaves, 105 days old, Postflowering drought stress, plot 4

description:
leaf_normCounts.txt
0914167L04


title: DBJS_SLIGRL_2

tag: treatment


title: BTX642 Leaves, 91 days old, Postflowering drought stress, plot 15

description:
leaf_normCounts.txt
0831165L15


title: DBJS_Vehicle_4

value: Vehicle


title: BTX642 Leaves, 91 days old, Postflowering drought stress, plot 4

description:
leaf_normCounts.txt
0831165L04


title: DBJS_Vehicle_2


title: BTX642 Leaves, 98 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0907166L21


title: BTX642 Leaves, 84 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0824164L21


title: MCF7_repl2

source_name: Breast cancer cell line

tag: cell line

value: Breast cancer cells

value: Full medium


title: DBJS_SLIGRL_1


title: BTX642 Leaves, 91 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0831165L21


title: DBJS_SLIGRL_3


title: BTX642 Leaves, 77 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0817163L21


title: DBJS_Vehicle_3


title: BTX642 Leaves, 77 days old, Postflowering drought stress, plot 15

description:
leaf_normCounts.txt
0817163L15


title: BTX642 Leaves, 77 days old, Postflowering drought stress, plot 4

description:
leaf_normCounts.txt
0817163L04


title: BTX642 Leaves, 112 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0921168L21


title: MCF7_aERa_repl2

tag: chip antibody

value: aERa (Santa Cruz, catalog# sc-543)


title: BTX642 Leaves, 70 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0810162L21


title: MCF7_aERa_repl1


title: DBJS_SLIGRL_4


title: MCF7_repl1


title: BTX642 Leaves, 70 days old, Postflowering drought stress, plot 4

description:
leaf_normCounts.txt
0810162L04


title: DBJS_Vehicle_1


title: BTX642 Leaves, 70 days old, Postflowering drought stress, plot 15

description:
leaf_normCounts.txt
0810162L15


title: ∆rnbΔrnr_RNA-Seq 1

city: Oeiras

first: Cecilia

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

data_processing:
Reads were mapped against E. coli genome (NC_000913 downloaded from NCBI genome database) using Bowtie2 program. The mapping files were sorted by genomic position using the Samtools and the quantification of the transcripts expression was done using the Artemis software.
Genome_build: NC_000913
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

organism: Escherichia coli K-12

source_name: Culture cells

growth_protocol: Overnight cultures from isolated colonies were diluted in fresh medium to an initial OD600~0.03 and grown to exponential phase (OD600~0.5) or stationary phase (16h growth) at 37ºC, with shaking at 200 rpm in Luria-Bertani (LB) medium supplemented with thymine (50 mg ml-1). When required, antibiotics were present at the following concentrations: kanamycin, 50 mg ml-1; tetracycline, 20 mg ml-1; streptomycin/spectinomycin 20 µg ml-1.

extract_protocol:
RNA was isolated following cell lysis and phenol:chloroform extraction as previously described (Andrade, Pobre et al. 2012). After precipitation step in ethanol and 300 mM sodium acetate, RNA was resuspended in MilliQ-water. The integrity of RNA samples was evaluated by agarose gel electrophoresis. Turbo DNase (Ambion) treatment was used to remove contaminant DNA.
RNA libraries were prepared for sequencing by the company Vertis Biotechnologie AG in Germany

tag: growth phase

value: Stationary Phase

value: RNase II/RNase R double mutant


title: BTX642 Leaves, 63 days old, Postflowering drought stress, plot 15

description:
leaf_normCounts.txt
0803169L15

tag: watering regime


title: BTX642 Leaves, 63 days old, Postflowering drought stress, plot 21

description:
leaf_normCounts.txt
0803169L21

tag: age (days)


title: ∆rnbΔrnr_RNA-Seq 2

value: Exponential phase


title: ∆pnp_RNA-Seq

value: PNPase mutant


title: BTX642 Leaves, 63 days old, Postflowering drought stress, plot 4

description:
leaf_normCounts.txt
0803169L04

tag: plot


title: ∆rnr_RNA-Seq

value: RNase R mutant


title: BTX642 Leaves, 119 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0928169L17

value: Preflowering drought stress


title: WT_RNA-Seq

value: Wild-type


title: ∆rnb_RNA-Seq

value: RNase II mutant


title: BTX642 Leaves, 105 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0914167L14


title: BTX642 Leaves, 112 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0921168L06


title: BTX642 Leaves, 105 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0914167L17


title: BTX642 Leaves, 84 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0824164L14


title: BTX642 Leaves, 105 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0914167L06


title: BTX642 Leaves, 84 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0824164L17


title: BTX642 Leaves, 98 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0907166L06


title: BTX642 Leaves, 84 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0824164L06


title: BTX642 Leaves, 119 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0928169L06


title: BTX642 Leaves, 70 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0810162L17


title: BTX642 Leaves, 77 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0817163L06


title: BTX642 Leaves, 70 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0810162L14


title: BTX642 Leaves, 77 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0817163L14


title: BTX642 Leaves, 91 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0831165L06


title: BTX642 Leaves, 91 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0831165L17


title: BTX642 Leaves, 77 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0817163L17


title: BTX642 Leaves, 91 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0831165L14


title: BTX642 Leaves, 63 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0803169L17


title: BTX642 Leaves, 119 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0928169L14


title: BTX642 Leaves, 63 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0803169L06


title: BTX642 Leaves, 63 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0803169L14


title: BTX642 Leaves, 56 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0727168L14


title: BTX642 Leaves, 56 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0727168L17


title: BTX642 Leaves, 49 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0720167L06


title: BTX642 Leaves, 42 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0713166L17


title: BTX642 Leaves, 42 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0713166L14


title: BTX642 Leaves, 42 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0713166L06


title: BTX642 Leaves, 35 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0706165L06


title: BTX642 Leaves, 35 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0706165L14


title: BTX642 Leaves, 28 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0629164L06


title: BTX642 Leaves, 70 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0810162L06


title: BTX642 Leaves, 21 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0622162L06


title: BTX642 Leaves, 28 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0629164L17


title: RTX430 Leaves, 119 days old, Control, plot 1

description:
leaf_normCounts.txt
0928169L01

value: Control


title: RTX430 Leaves, 119 days old, Control, plot 12

description:
leaf_normCounts.txt
0928169L12


title: RTX430 Leaves, 105 days old, Control, plot 12

description:
leaf_normCounts.txt
0914167L12


title: RTX430 Leaves, 105 days old, Control, plot 20

description:
leaf_normCounts.txt
0914167L20


title: BTX642 Leaves, 21 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0622162L14


title: RTX430 Leaves, 112 days old, Control, plot 12

description:
leaf_normCounts.txt
0921168L12


title: RTX430 Leaves, 98 days old, Control, plot 12

description:
leaf_normCounts.txt
0907166L12


title: RTX430 Leaves, 91 days old, Control, plot 12

description:
leaf_normCounts.txt
0831165L12


title: meningioma [16-42]

city: Houston

first: Tiemo

middle: J

last: Klisch

state: Texas

address: 1250 Moursund Street, N1370.08

department: Department of Molecular and Human Genetics

institute: Baylor College of Medicine

description:
16-42
1st Recurrence of DCC40

data_processing:
Individual libraries within the samples were demultiplexed using CASAVA 1.8.2 (CASAVA, RRID:SCR_001802).
TopHat2 (RRID:SCR_013035) was used for read alignment.
FastQC (RRID:SCR_014583) and RSeQC (RRID:SCR_005275) were used for read and alignment quality assessment.
HTSeq (RRID:SCR_005514) was used for expression count.
The reads were aligned to GRCh37 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations.
Genome_build: GRCh37
Supplementary_files_format_and_content: *_htseq.counts.txt: Tab-delimited text files include expression count values for each Sample.

source_name: meningioma, WHO II, Recurrence

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit (Qiagen).
Illumina, using SOP from BCM-HGSC (https://www.hgsc.bcm.edu).

tag: cohort

value: Recurrence

tag: tissue

value: Meningioma

tag: pathology

value: WHO II

tag: gender

value: not determined

tag: age

tag: wes


title: RTX430 Leaves, 91 days old, Control, plot 1

description:
leaf_normCounts.txt
0831165L01


title: BTX642 Leaves, 56 days old, Preflowering drought stress, plot 6

description:
leaf_normCounts.txt
0727168L06


title: BTX642 Leaves, 28 days old, Preflowering drought stress, plot 14

description:
leaf_normCounts.txt
0629164L14


title: meningioma [16-32]

description:
16-32
1st Recurrence of 15-11

source_name: meningioma, WHO I, Recurrence

value: WHO I


title: RTX430 Leaves, 84 days old, Control, plot 12

description:
leaf_normCounts.txt
0824164L12


title: BTX642 Leaves, 35 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0706165L17


title: meningioma [18-51]

description:
18-51
1st Recurrence of 17-33


title: meningioma [18-19]

description:
18-19
1st Recurrence of 16-30


title: meningioma [18-02]

description:
18-02
1st Recurrence of DCC11, tumor 2

source_name: meningioma, WHO III, Recurrence

value: WHO III


title: meningioma [16-39]

description:
16-39
1st Recurrence of 16-28


title: meningioma [16-46]

description:
16-46
1st Recurrence of 15-13


title: RTX430 Leaves, 119 days old, Control, plot 20

description:
leaf_normCounts.txt
0928169L20


title: RTX430 Leaves, 84 days old, Control, plot 1

description:
leaf_normCounts.txt
0824164L01


title: BTX642 Leaves, 21 days old, Preflowering drought stress, plot 17

description:
leaf_normCounts.txt
0622162L17


title: meningioma [18-01]

description:
18-01
1st Recurrence of DCC11, tumor 1


title: RTX430 Leaves, 77 days old, Control, plot 1

description:
leaf_normCounts.txt
0817163L01


title: RTX430 Leaves, 77 days old, Control, plot 12

description:
leaf_normCounts.txt
0817163L12


title: RTX430 Leaves, 77 days old, Control, plot 20

description:
leaf_normCounts.txt
0817163L20


title: meningioma [17-14]

description:
17-14
3rd Recurrence of DCC14


title: meningioma [DCC39]

description:
DCC39
1st Recurrence of DCC14


title: RTX430 Leaves, 70 days old, Control, plot 20

description:
leaf_normCounts.txt
0810162L20


title: RTX430 Leaves, 70 days old, Control, plot 1

description:
leaf_normCounts.txt
0810162L01


title: meningioma [15-30]

description:
15-30
2nd Recurrence of DCC04, tumor 2


title: RTX430 Leaves, 70 days old, Control, plot 12

description:
leaf_normCounts.txt
0810162L12


title: meningioma [15-29]

description:
15-29
2nd Recurrence of DCC04, tumor 1


title: meningioma [15-10]

description:
15-10
1st Recurrence of DCC04


title: RTX430 Leaves, 63 days old, Control, plot 20

description:
leaf_normCounts.txt
0803169L20


title: RTX430 Leaves, 63 days old, Control, plot 1

description:
leaf_normCounts.txt
0803169L01


title: RTX430 Leaves, 63 days old, Control, plot 12

description:
leaf_normCounts.txt
0803169L12


title: meningioma [18-47]

description:
18-47
Primary tumor

source_name: meningioma, WHO I, Validation

value: Validation

value: Female

value: Y


title: meningioma [18-46]

description:
18-46
Primary tumor

source_name: meningioma, WHO II, Validation


title: RTX430 Leaves, 42 days old, Control, plot 20

description:
leaf_normCounts.txt
0713166L20


title: RTX430 Leaves, 42 days old, Control, plot 1

description:
leaf_normCounts.txt
0713166L01


title: RTX430 Leaves, 42 days old, Control, plot 12

description:
leaf_normCounts.txt
0713166L12


title: RTX430 Leaves, 49 days old, Control, plot 12

description:
leaf_normCounts.txt
0720167L12


title: RTX430 Leaves, 56 days old, Control, plot 20

description:
leaf_normCounts.txt
0727168L20


title: RTX430 Leaves, 56 days old, Control, plot 12

description:
leaf_normCounts.txt
0727168L12


title: RTX430 Leaves, 35 days old, Control, plot 20

description:
leaf_normCounts.txt
0706165L20


title: RTX430 Leaves, 91 days old, Control, plot 20

description:
leaf_normCounts.txt
0831165L20


title: meningioma [18-04]

description:
18-04
4th Recurrence of DCC14


title: RTX430 Leaves, 35 days old, Control, plot 1

description:
leaf_normCounts.txt
0706165L01


title: RTX430 Leaves, 28 days old, Control, plot 1

description:
leaf_normCounts.txt
0629164L01


title: RTX430 Leaves, 28 days old, Control, plot 20

description:
leaf_normCounts.txt
0629164L20


title: meningioma [18-10]

description:
18-10
Primary tumor

value: Male


title: meningioma [15-28]

description:
15-28
2nd Recurrence of DCC14


title: RTX430 Leaves, 28 days old, Control, plot 12

description:
leaf_normCounts.txt
0629164L12


title: meningioma [17-31]

description:
17-31
Primary tumor


title: RTX430 Leaves, 21 days old, Control, plot 12

description:
leaf_normCounts.txt
0622162L12


title: RTX430 Leaves, 21 days old, Control, plot 1

description:
leaf_normCounts.txt
0622162L01


title: RTX430 Leaves, 21 days old, Control, plot 20

description:
leaf_normCounts.txt
0622162L20


title: RTX430 Leaves, 14 days old, Control, plot 20

description:
leaf_normCounts.txt
0615163L20


title: RTX430 Leaves, 14 days old, Control, plot 1

description:
leaf_normCounts.txt
0615163L01


title: RTX430 Leaves, 119 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0928169L22

value: Postflowering drought stress


title: RTX430 Leaves, 119 days old, Postflowering drought stress, plot 16

description:
leaf_normCounts.txt
0928169L16


title: RTX430 Leaves, 105 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0914167L22


title: RTX430 Leaves, 105 days old, Postflowering drought stress, plot 16

description:
leaf_normCounts.txt
0914167L16


title: RTX430 Leaves, 105 days old, Postflowering drought stress, plot 3

description:
leaf_normCounts.txt
0914167L03


title: RTX430 Leaves, 56 days old, Control, plot 1

description:
leaf_normCounts.txt
0727168L01


title: RTX430 Leaves, 77 days old, Postflowering drought stress, plot 16

description:
leaf_normCounts.txt
0817163L16


title: RTX430 Leaves, 98 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0907166L22


title: RTX430 Leaves, 91 days old, Postflowering drought stress, plot 3

description:
leaf_normCounts.txt
0831165L03


title: RTX430 Leaves, 84 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0824164L22


title: RTX430 Leaves, 91 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0831165L22


title: meningioma [17-21]

description:
17-21
Primary tumor


title: RTX430 Leaves, 77 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0817163L22


title: meningioma [18-21]

description:
18-21
Primary tumor


title: RTX430 Leaves, 70 days old, Postflowering drought stress, plot 3

description:
leaf_normCounts.txt
0810162L03


title: meningioma [17-26]

description:
17-26
Primary tumor


title: RTX430 Leaves, 63 days old, Postflowering drought stress, plot 16

description:
leaf_normCounts.txt
0803169L16


title: RTX430 Leaves, 70 days old, Postflowering drought stress, plot 16

description:
leaf_normCounts.txt
0810162L16


title: RTX430 Leaves, 63 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0803169L22


title: RTX430 Leaves, 77 days old, Postflowering drought stress, plot 3

description:
leaf_normCounts.txt
0817163L03


title: RTX430 Leaves, 119 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0928169L18


title: RTX430 Leaves, 91 days old, Postflowering drought stress, plot 16

description:
leaf_normCounts.txt
0831165L16


title: RTX430 Leaves, 119 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0928169L13


title: meningioma [17-32]

description:
17-32
Primary tumor


title: RTX430 Leaves, 98 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0907166L05


title: RTX430 Leaves, 14 days old, Control, plot 12

description:
leaf_normCounts.txt
0615163L12


title: RTX430 Leaves, 119 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0928169L05


title: RTX430 Leaves, 91 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0831165L05


title: RTX430 Leaves, 91 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0831165L18


title: RTX430 Leaves, 84 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0824164L05


title: RTX430 Leaves, 91 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0831165L13


title: meningioma [DCC57]

description:
DCC57
Primary tumor

source_name: meningioma, WHO II, Discovery

value: Discovery


title: RTX430 Leaves, 77 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0817163L05


title: RTX430 Leaves, 84 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0824164L13


title: RTX430 Leaves, 70 days old, Postflowering drought stress, plot 22

description:
leaf_normCounts.txt
0810162L22


title: RTX430 Leaves, 77 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0817163L13


title: meningioma [16-33]

description:
16-33
Primary tumor

source_name: meningioma, WHO I, Discovery


title: RTX430 Leaves, 70 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0810162L05


title: RTX430 Leaves, 63 days old, Postflowering drought stress, plot 3

description:
leaf_normCounts.txt
0803169L03


title: RTX430 Leaves, 63 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0803169L18


title: meningioma [16-29]

description:
16-29
Primary tumor


title: RTX430 Leaves, 63 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0803169L05


title: meningioma [14-02]

description:
14-02
Primary tumor


title: RTX430 Leaves, 112 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0921168L05


title: RTX430 Leaves, 63 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0803169L13


title: RTX430 Leaves, 70 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0810162L13


title: RTX430 Leaves, 56 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0727168L05


title: meningioma [DCC56]

description:
DCC56
Primary tumor


title: RTX430 Leaves, 56 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0727168L18


title: RTX430 Leaves, 105 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0914167L05


title: RTX430 Leaves, 49 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0720167L05


title: meningioma [DCC14]

description:
DCC14
Primary tumor


title: meningioma [DCC17]

description:
DCC17
Primary tumor


title: RTX430 Leaves, 42 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0713166L13


title: RTX430 Leaves, 84 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0824164L18


title: RTX430 Leaves, 56 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0727168L13


title: RTX430 Leaves, 77 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0817163L18


title: meningioma [DCC20]

description:
DCC20
Primary tumor


title: RTX430 Leaves, 35 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0706165L13


title: RTX430 Leaves, 42 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0713166L05


title: RTX430 Leaves, 35 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0706165L05


title: RTX430 Roots, 84 days old, Control, plot 20

description:
root_normCounts.txt
0824164R20


title: RTX430 Leaves, 84 days old, Control, plot 20

description:
leaf_normCounts.txt
0824164L20


title: RTX430 Leaves, 28 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0629164L18


title: RTX430 Roots, 84 days old, Preflowering drought stress, plot 13

description:
root_normCounts.txt
0824164R13


title: RTX430 Leaves, 35 days old, Control, plot 12

description:
leaf_normCounts.txt
0706165L12


title: meningioma [DCC54]

description:
DCC54
Primary tumor


title: RTX430 Roots, 35 days old, Control, plot 20

description:
root_normCounts.txt
0706165R20


title: RTX430 Leaves, 42 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0713166L18


title: RTX430 Leaves, 119 days old, Postflowering drought stress, plot 3

description:
leaf_normCounts.txt
0928169L03


title: Nuybai

city: Ottawa

first: Ziying

last: Liu

state: ON

address: 1200 Montreal Road

country: Canada

institute: National Research Council, Canada

description: wheat treated with F. graminearum inoculation 2days

data_processing:
RNA-seq reads were preprocessed by trimming the adaptor sequences, filtering low-quality reads (Phred Score <=20 [Phred]) and eliminating short reads (length <= 20 bps) using software package from Stanford University (http://sfg.stanford.edu/)
RAN-seq reads were aligned to the pan-genome of Chinese Spring (IWGSC RefSeq v1.0) from the IWGSC sequence repository hosted by URGI-INRA (https://wheat-urgi.versailles.inra.fr/) and Fusarium graminearum reference genome (Fusarium graminearum str. PH-1) from EnsemblFungi (http://fungi.ensembl.org/, Release 35) using STAR v2.5.3a
R package DESeq2 was used for data normalization and to generate differentially expressed gene (DEG)
Genome_build: IWGSC RefSeq v1.0; Fusarium graminearum str. PH-1
Supplementary_files_format_and_content: Raw read counts data

organism: Triticum aestivum

source_name: whole head

growth_protocol: Eighty-five doubled haploid lines derived from the cross Wuhan-1/Nyubai and the two parents were grown in controlled-environment cabinets with 16h light at 20°C and 8h dark at 16°C until mid-anthesis.

extract_protocol:
Total RNA was extracted using the TRI-Reagent (Molecular Research Center Inc) following manufacturer’s instructions, except for the following modification: the aqueous phase separation was technically implemented with phase-lock gel tubes (5 PRIME Inc., Gaithersburg, MD, USA) before the isopropanol precipitation. Crude total RNAs were cleaned up using the RNeasy Mini Kit (Qiagen, Mississauga, Canada), including a DNase I treatment from RNase-free DNase set (Qiagen), according to manufacturer’s instructions. RNA integrity and quality were initially tested by separation on denaturing 1% formaldehyde agarose gel electrophoresis; quantification and additional quality evaluation were performed using the QIAxpert instrument (Qiagen, Missisauga, Canada). RNA was processed for deep paired-end RNA sequencing (RNA-seq) using Illumina HiSeq 2500
Libraries were prepared according to Illumina's instructions, using the TruSeq RNA v2 LT kit and sequenced on the Genome Analyzer following the manufacturer's protocols (https://www.illumina.com/documents/products/datasheets/datasheet_hiseq2500.pdf).

treatment_protocol: Heads at mid-anthesis were point inoculated with 10 μL of a F. graminearum (strain DAOM233423, Collection of Fungal Cultures, Agriculture and Agri-Food Canada, Ottawa, Canada) macroconidial spore suspension at 1 x 105 spores/mL using a micropipette between the lemma and palea of two basal florets of each fully developed spikelet on each treated head. Following inoculation, plants were transferred into another growth chamber where they were misted overhead; pots were disposed in a random order. Misting was for two days, 30 sec every 1 h, during the light period. Inoculated heads were collected at 2 dpi and 5 to 6 whole heads were pooled into one sample per DH line.

value: Nuybai

value: whole head

value: F. graminearum

tag: sample taken (dpi)


title: HC 536

tag: genotype

value: Wuhan x Nuybai


title: RTX430 Leaves, 28 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0629164L05

value: Preflowering drought stress


title: RTX430 Leaves, 21 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0622162L18


title: RTX430 Leaves, 70 days old, Preflowering drought stress, plot 18

description:
leaf_normCounts.txt
0810162L18


title: HC 521


title: RTX430 Leaves, 28 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0629164L13


title: meningioma [DCC11]

description:
DCC11
Primary tumor


title: HC 520


title: meningioma [16-30]

description:
16-30
Primary tumor


title: HC 512


title: meningioma [DCC49]

description:
DCC49
Primary tumor


title: meningioma [DCC55]

description:
DCC55
Primary tumor


title: RTX430 Leaves, 21 days old, Preflowering drought stress, plot 13

description:
leaf_normCounts.txt
0622162L13


title: meningioma [DCC50]

description:
DCC50
Primary tumor


title: HC 503


title: HC 504


title: RTX430 Leaves, 21 days old, Preflowering drought stress, plot 5

description:
leaf_normCounts.txt
0622162L05


title: HC 497


title: HC 501


title: HC 498


title: Wuhan

value: Wuhan


title: HC 500


title: HomFib3

city: Beijing

first: Yang

address: 30 Xueyuan Road, Haidian District

institute: University of Science and Technology Beijing

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Ensemble_GRCm38.90 whole genome using tophat2  with parameters  -p 8 -N 2 --read-edit-dist 2
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. Then we used the DESeq2 R package (1.20.0) in R to analyze the differential expression of two conditions/groups (three biological replicates per condition).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 values for each Sample ...

source_name: Normal human dermal fibroblasts

extract_protocol:
A small number of HT1080 cells and fibroblast cells (20-50 cells) were manually retrieved from the schematic features by using a mouth pipette with a self-pulled capillary (tip open about 40 μm) after coculturing for 24h. Labeled with different kind of cell-tracker dyes, these two types of cells have been observed under a fluorescence microscope (AZ100, Nikon, Japan) to distinguish target cell types, and then transferred into PCR tubes from mouth pipet for cell lysis. cDNA were further purified by QIAquick PCR purification kit.0.5-5 kb fragments were excised from agarose gel electrophoresis and purified by QIAquick gel extraction kit. Then each sample was amplified by another 10 cycles of PCR using amine-blocked primers (95 °C for 3 min, then 10 cycles of 95 °C for 30 s, 67 °C for 1 min and 72 °C for 6min (+6 s each cycle) with a 4 °C and hold). After the second purification, products were used for sequencing library preparation.
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.

value: derma

tag: cell type

value: NHDF (Homoculture)

tag: developmental stage

value: the fourth-tenth generation

tag: culture condition

value: single cultivation


title: HomFib2


title: HomFib1


title: meningioma [DCC04]

description:
DCC04
Primary tumor

value: Meningioma

value: WHO II


title: CoFib3

value: NHDF (Coculture with HT1080)

value: coculture with HT1080 cells 24h


title: HC 494

tag: treatment


title: HC 492


title: HC 508


title: HC 491


title: HC 486


title: HC 488


title: CoFib2


title: HC 487


title: HC 485